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Intense research has been carried out into methods that aim at harvesting fetal cells from maternal blood as substitutes to amniocentesis and chorionic villus sampling. This work focuses on the separation of fetal nucleated red blood cells from the maternal circulation based on their intrinsic magnetic properties. The design and simulation of a magnetophoretic separator is described, as it will be one of the stages of a lab-on-chip for Non-Invasive Prenatal Diagnosis (NIPD). Finite element analyses have been used to assist design choices and to confirm analytical results. A final layout has been validated for manufacturing and testing. Successful fabrication and positive test results of the device will constitute a further step towards the implementation of new techniques for NIPD.